BBC director general Mark Thompson wants to cut £400m from budgets in the wake of the licence fee freeze. Photograph: Peter Macdiarmid/Getty Images

The BBC is wasting nearly £80m a year through poor management of under-performing staff and erroneously paying a salary top-up to thousands of employees who do not qualify for it, an internal report has concluded.

More than 1,000 job cuts have already been announced by the BBC from the World Service and its online operation and several thousand more are expected – up to 25% of the total workforce of about 22,000 – as part of the cost cutting in the coming years.

Poorly performing staff were costing the corporation more than £50m a year, according to the report, which recommended the introduction of a new management appraisal system based on conversations rather than paperwork.

The report categorised 910 staff – about 5% of the BBC's total workforce – as "poor performers" and said fewer than half of nearly 3,000 employees in the BBC Vision division, which spans all of the BBC's TV channels, were given a regular appraisal.

Other issues identified in the report include £28m in "unpredictability allowances" paid annually to BBC staff who did not work unpredictable hours. The total cost of the unpredictability allowance scheme of £33m a year made up more than 3% of the corporation's annual wage bill of about £1bn.

The study was put together by the People department as part of the BBC's "Delivering Quality First" initiative in which staff are invited to put forward their ideas on cost savings and how the corporation can provide the best quality programmes for its audience.

A BBC spokesperson said: "No decisions have been made so it would be wrong to speculate. It is of course only right that BBC staff have an opportunity to input ideas about shaping the BBC's future.

"These sessions are designed to provoke discussion amongst staff about the way the BBC works and any decisions coming out of the DQF process would be subject to public consultation by the BBC Trust."

The People department report also suggested a big discrepancy in pay between different parts of the corporation. Staff between pay grades seven and nine in BBC Vision earned an average of £40,436, 10% more than the typical pay for people on the same pay grades in the BBC News department, who earned an average of £36,464.

Staff at equivalent pay grades in the corporation's operations department, responsible for strategy, property and legal affairs, earned an average of £46,916.

The document is understood to have recommended a more flexible BBC workforce with more people on short-term contracts, fewer long-term "lifers" and less generous redundancy terms.

"People don't leave the BBC, they leave line managers," said the report. "50% of the organisation has a turnover of just 3%. Some areas have even less. When considering the employee deal, it's more productive to start from identifying what it's not. It's not a job for life, a gold-plated pension [or] a paternalistic institution (any more)."

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